The binding site of sodium in the gramicidin A channel: Comparison of molecular dynamics with solid-state NMR data

The location of the main binding site for sodium in the gramicidin A (GA) channel was investigated with molecular dynamics simulations, using an atomic model of the channel embedded in a fully hydrated dimyristoyl phosphatidycholine (DMPC) bilayer. Twenty-four separate simulations in which a sodium was restrained at different locations along the channel axis were generated. The results are compared with carbonyl C-13 chemical shift anisotropy solid-state NMR experimental data previously obtained with oriented GA:DMPC samples, Predictions are made for other solid-state NMR properties that could be observed experimentally. The combined information from experiment and simulation strongly suggests that the main binding sites for sodium are near the channel's mouth, approximately 9.2 Angstrom from the center of the dimer channel. The C-13 chemical shift anisotropy of Leu(10) is the most affected by the presence of a sodium ion in the binding site. In the binding site, the sodium ion is lying off-axis, making contact with two carbonyl oxygens and two single-file water molecules. The main channel ligand is provided by the carbonyl group of the Leu(10)-Trp(11) peptide linkage, which exhibits the largest deviation from the ion-free channel structure. Transient contacts with the carbonyl group of Val(8) and Trp(15) are also present. The influence of the tryptophan side chains on the channel conductance is examined based on the current information about the binding site.